replace empties with 2 bones armature in script
This can be achieved adding one line and changing another(variables changed so it makes sense):

import bpy
import bmesh

context = bpy.context
scene = context.scene
obj = context.edit_object
mesh = obj.data
bm = bmesh.from_edit_mesh(mesh)
armature =bpy.data.objects['Armature'] #added this line to get armature object
armatures = []
# selected verts
for v in [v for v in bm.verts if v.select]:
    bones = armature.copy() # changed this line to mke copies
    bones.parent = obj
    bones.parent_type = 'VERTEX'
    bones.parent_vertices = [v.index] * 3
    scene.objects.link(bones)
    bones.matrix_parent_inverse.identity()
    armatures.append((v.index, bones))